Method for screening special species by comprehensively applying richness-distribution index and random inspection

Abstract

The invention relates to screening of special species of ecological communities in different environments, and provides a method for screening special species of communities by comprehensively applying richness-distribution indexes and random inspection. According to the method, a richness-distribution index and random inspection are comprehensively applied, random differences between samples among groups and between samples in the groups are eliminated, and specific species and dominant species of the environment are screened out. The screened specific species and dominant species can be used as environmental markers, and the colonies can be typed through the special species. The ecological communities involved in the invention comprise macroscopic ecological communities (such as farmlands, orchards, forests, grassland, coral reefs and the like) and microbial ecological communities (animals, plants and environmental microorganisms, especially human flora micro-ecological communities). For a macroscopic ecological community, the screened special species can be used as a monitoring index of an environmental state. For the microscopic ecological community, the screened special species can be used as an index for monitoring the state of the host and diagnosing diseases.

Description

Technical Field

[0001] The present invention relates to a method for screening special species in ecological communities under different environments or hosts, and in particular, to a method for defining and screening special species in communities by comprehensively applying richness-distribution indexes and random inspection methods. Each species richness-distribution index of the community is quantitatively evaluated, and special species in the community are screened out, including community-specific species and dominant species in the community (species with significantly increased richness-distribution indexes relative to other communities). In macroscopic ecological communities, this method can be used for scientific decision-making in the prediction and prevention of pests and diseases in crops, vegetables, orchards, and economic forests. In microscopic ecological communities, species specific to communities under different host conditions can be screened as indicators for host status monitoring and disease diagnosis and treatment indicators. Background Art

[0002] Species diversity in a community is a basic indicator for describing the state of a community. Diversity not only describes the number of species in a community, but also reflects the difference in the number of individuals of each species (i.e., relative richness). However, there is a major flaw in comparing the differences between communities through species diversity, which is that the differences between species themselves are ignored, and only the difference in number between species can be described. For example, the diversity index does not reflect the difference in the important characteristic of species distribution range. This defect is not fatal at the community level, but it becomes an intolerable fatal defect at the metacommunity level. Metacommunity can be simply understood as "community of communities"; that is, communities are composed of species, and metacommunities are composed of communities. Obviously, at the metacommunity level, the differences between species in each metacommunity are not only reflected in relative abundance, but also in the breadth of their distribution, i.e., the frequency of species distribution. Therefore, the above two factors should be considered comprehensively when evaluating species diversity.

[0003] In the human microbial community, the comprehensive evaluation of microbial species diversity and specificity is used to diagnose human microbial-related diseases and predict their risk of occurrence. The human intestinal tract, oral cavity, skin, respiratory tract, and reproductive tract are the main "stationing" sites of microbial flora, which are closely related to human health and disease. Thousands of microorganisms distributed in these sites carry a large amount of genetic information, and the number of genes they carry even far exceeds the number of genes in the human body itself. Since 2001, the completion of the "Human Genome Project" has greatly promoted the rapid development and application of sequencing technology, and sequencing technology has been widely used in various fields of life sciences and biotechnology. Metagenomic sequencing technology is a sequencing method for microbial flora, which makes it possible to identify species and analyze genetic information of massive microorganisms. In 2007, the National Institutes of Health (NIH) of the United States launched the "Human Microbiome Research Program (HMP)" to study the composition of human microbial flora and its impact on human diseases. In May 2016, the White House of the United States announced the launch of the "National Microbiome Initiative (NMI)". The difference between the latter US program (NMI) and the completed HMP program is that the latest NMI program emphasizes "action", especially technology development and industrialization. The European Union also has a similar research program (MetaHIT) and has achieved similar success. It can be predicted that the competition for microbial flora research at home and abroad will become more intense. Summary of the invention

[0005] The objects of the present invention are: Comprehensive richness-distribution index and random test to screen special species in the community. For example, two groups of community samples under environment A and environment B, through the richness-distribution index index, screen the special species of the community. Special species include: unique species of environment A, unique species of environment B, dominant species of environment A (species with significantly increased richness-distribution index relative to environment B), dominant species of environment B (species with significantly increased richness-distribution index relative to environment A). The biggest advantage of random test is that it can exclude the influence of random differences between samples within and between groups. Through random test, the influence of sample differences can be excluded, and the special species screened out are only affected by environmental factors. Therefore, the species unique to environment A screened out can be used as special markers of environment A, and the species with significantly increased richness-distribution index of environment A relative to environment B are species selected by the special environment of environment A. For example, in microbial communities, the method of the invention can be used to screen out unique species in different environments (forests, oceans, soils, hot springs, rivers, lakes) and different hosts (human body, animals, plants) as indicators for monitoring the state of the environment or host.

[0006] The technical solution adopted by the present invention is: For the two groups of samples in environment A and environment B, the process of applying random testing to screen special species is as follows: first, the species richness-distribution index is calculated according to formulas (1)-(4): represents the distribution extent of the i-th species in the metacommunity h, It represents the relative abundance of the i-th species in metacommunity h among all H metacommunities. Therefore, the richness-distribution index evaluates species by combining the distribution frequency and relative abundance of species in metacommunities. S1: Calculate the richness-distribution index of each species in environment A and environment B respectively, and calculate the absolute value Δ of the difference in the richness-distribution index of each species in environment A and environment B; S2: Mix samples from environment A and environment B, randomly divide them into two groups A' and B', calculate the richness-distribution index of each species in the two groups of samples A' and B', and calculate the absolute value Δ' of the difference in the richness-distribution index of each species in A' and B'; S3: Repeat step S2 1000 times to obtain 1000 Δ's; S4: Calculate the p value of each species according to the formula p = n / 1000, where n represents the number of 1000 Δ's greater than Δ in S3; S5: Species unique to environment A must meet the following conditions: p < 0.05, the richness-distribution index in environment A is not equal to 0, and the richness-distribution index in environment B is equal to 0; S6: Species unique to environment B must meet the following conditions: p < 0.05, the richness-distribution index in environment B is not equal to 0, and the richness-distribution index in environment A is equal to 0; S7: The dominant species in environment A (species with significantly higher richness-distribution indexes than those in environment B) must meet the following conditions: p < 0.05, the richness-distribution indexes in both environments A and B are not equal to 0, and the richness-distribution index in environment A is greater than that in environment B; S8: The dominant species in environment B (species with significantly higher richness-distribution indexes than those in environment A) must meet the following conditions: p < 0.05, the richness-distribution indexes in both environments A and B are not equal to 0, and the richness-distribution index in environment B is greater than that in environment A;

[0007] The effects of the present invention are: A method for screening special species in a community by comprehensive application of richness-distribution index and random test is invented. The effects achieved by the present invention include: screening special species in an environmental community by eliminating the differences between samples within and between groups through random test. The special species in the community include: species unique to the environment and significantly dominant species in the environment. The screened special species can be used as an indicator to monitor the state of the environment or the host.

[0008] Figure 1 It is a flowchart for screening special species. First, the richness-distribution index of each species is calculated according to the formula, and then the richness-distribution index of the species is randomly tested to screen special species. DETAILED DESCRIPTION

[0009] The present invention takes the intestinal microbial samples of two types of hosts, Aves and Mammals, as examples, and screens out species unique to the intestinal tract of Aves, species unique to the intestinal tract of Mammals, dominant species in Aves relative to Mammals, and dominant species in Mammals relative to Aves through random testing. According to a specific embodiment of the present invention, the calculation process is as follows: S1: Calculate the richness-distribution index of each species in the intestinal microorganisms of the class Aves and the environmental microorganisms of the class Mammalian, and calculate the absolute value Δ of the difference in the richness-distribution index of each species in the class Aves and the class Mammalian; S2: Mix the intestinal microbial samples of birds and mammals, and randomly divide them into two groups A' and B'. Calculate the richness-distribution index of each species in the two groups A' and B', and calculate the absolute value Δ' of the difference in the richness-distribution index of each species in A' and B'; S3: Repeat step S2 1000 times to obtain 1000 Δ's; S4: Calculate the p value of each species according to the formula p = n / 1000, where n represents the number of 1000 Δ's greater than Δ in S3; S5: The microorganisms unique to the gut of Aves must meet the following conditions: p < 0.05, the richness-distribution index in Aves is not equal to 0, and the richness-distribution index in Mammals is equal to 0; S6: Microorganisms unique to the class Mammalia must meet the following conditions: p < 0.05, the richness-distribution index in the class Mammalia is not equal to 0, and the richness-distribution index in the class Aves is equal to 0; S7: The dominant microorganisms in Aves relative to Mammals must meet the following conditions: p < 0.05, the richness-distribution index in both Aves and Mammals is not equal to 0, and the richness-distribution index in Aves is greater than that in Mammals; S8: The dominant species in Mammals relative to Aves must meet the following conditions: p < 0.05, the abundance-distribution index in both Aves and Mammals is not equal to 0, and the abundance-distribution index in Mammals is greater than that in Aves;

[0010] According to the above steps, the present invention screened out microorganisms unique to the intestinal tract of the class Aves, microorganisms unique to the intestinal tract of the class Mammalian, microorganisms with significantly increased abundance-distribution indexes of the class Aves relative to the class Mammalian, and microorganisms with significantly increased abundance-distribution indexes of the class Mammalian relative to the class Aves through random testing. Table 1 lists some of the special species of the two classes Table 1. List of special microorganisms in Aves and Mammals Endemic species of birds Endemic species of mammals Dominant species of Aves Mammal dominant species OD1_73 platynotus_115 Methylophilaceae_91 Myroides_63 Myroides_6 Bacillus_61 Bacillus_93 OD1_75 OD1_19 Planctomyces_4 OD1_53 Bacteria_34 OD1_64 OD1_15 Ralstonia_102 Entomoplasmatales_10 Comamonadaceae_70 meningoseptica_11 OD1_38 OD1_41 Bacteria_80 OD1_110 Entomoplasmatales_29 massiliensis_122 Comamonadaceae_120 multivorum_14 acidaminiphila_52 Wolbachia_96 muralis_86 Solibacillus_99 meningoseptica_81 Stenotrophomonas_55 OD1_97 Wolbachia_21 OD1_76 OD1_23 OD1_103 Bacteria_9 Xanthobacter_7 OD1_22 Paenibacillus_31 Methylophilaceae_40 OD1_89 Legionella_28 Flavobacterium_59 OD1_88 Planococcaceae_3 OD1_2 Legionellaceae_107 OD1_100 faecium_51 Leucobacter_68 platynotus_94 Achromobacter_1 Wautersiella_39 Bacillus_30 Enterococcaceae_13 Lactobacillales_114 OD1_42 Flavobacteriales_77 Ochrobactrum_58 OD1_65 Wolbachia_78 OD1_101 Swaminathania_71 Rhizobiaceae_18 OD1_108 OD1_62 OD1_117 OD1_109 Wolbachia_47 OD1_33 OD1_35 Wolbachia_84 OD1_121 OD1_118 multivorans_98 OD1_49 platynotus_57 OD1_104

Claims

1. A method for screening special species in communities by comprehensive application of richness-distribution index and random inspection, for two different environments A and B, the special species in the community include: Species unique to environment A, species unique to environment B, dominant species in environment A, i.e. species with significantly higher richness-distribution index than that in environment B, dominant species in environment B, i.e. species with significantly higher richness-distribution index than that in community A, characterized in that for two groups of community samples in environment A and environment B, the following steps are applied to screen community-specific species: S1: Calculate the richness-distribution index of each species in environment A and environment B respectively, and calculate the absolute value Δ of the difference in richness-distribution index of each species in environment A and environment B; S2: Mix samples from environment A and environment B, randomly divide them into two groups A' and B', calculate the richness-distribution index of each species in the two groups of samples A' and B', and calculate the absolute value Δ' of the difference in richness-distribution index of each species in A' and B'; S3: Repeat step S2 1000 times to obtain 1000 Δ's; S4: Calculate the p value of each species according to the formula p = n / 1000, where n represents the number of 1000 Δ's greater than Δ in S3; S5: Species unique to environment A must meet the following conditions: p < 0.05, the richness-distribution index in environment A is not equal to 0, and the richness-distribution index in environment B is equal to 0; S6: Species unique to environment B must meet the following conditions: p < 0.05, the richness-distribution index in environment B is not equal to 0, and the richness-distribution index in environment A is equal to 0; S7: The dominant species in environment A must meet the following conditions: p < 0.05, the richness-distribution index in both environment A and B is not equal to 0, and the richness-distribution index in environment A is greater than that in environment B; S8: The dominant species in environment B must meet the following conditions: p < 0.05, the richness-distribution index in both environments A and B is not equal to 0, and the richness-distribution index in environment B is greater than the richness-distribution index in environment A.

2. The method according to claim 1, characterized in that: The richness-distribution index is an indicator that combines species richness and species distribution frequency.

3. The method according to claim 1, characterized in that: Environment A and environment B represent both the macroecological community environment and the host environment of the microbial community.

4. The method according to claim 1, characterized in that: The random test method was applied to test each species in the environment, and the test results showed that the richness-distribution indicators of specific species were significantly different between different environments.

5. The method according to claims 1-4, characterized in that: Products that implement their algorithms and functions in any form of software, firmware and hardware to provide services.

Images